Query         gi|254780320|ref|YP_003064733.1| translation initiation factor IF-3 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 136
No_of_seqs    113 out of 1373
Neff          5.6 
Searched_HMMs 39220
Date          Sun May 29 15:41:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780320.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG0290 InfC Translation initi 100.0       0       0  359.6  13.3  136    1-136    40-175 (176)
  2 CHL00199 infC translation init 100.0       0       0  357.5  15.0  136    1-136    46-181 (182)
  3 PRK00028 infC translation init 100.0       0       0  337.1  15.0  135    1-135    39-173 (175)
  4 TIGR00168 infC translation ini 100.0 3.4E-30 8.6E-35  201.1  10.3  135    1-135    29-164 (165)
  5 pfam00707 IF3_C Translation in 100.0   5E-30 1.3E-34  200.1   9.9   87   48-134     1-87  (87)
  6 pfam05198 IF3_N Translation in  99.7 1.9E-17 4.9E-22  125.0   4.5   43    1-43     34-76  (76)
  7 pfam06152 Phage_min_cap2 Phage  56.2     7.1 0.00018   20.3   1.8   25    2-26    217-242 (361)
  8 COG5014 Predicted Fe-S oxidore  45.4      10 0.00026   19.4   1.2   96    1-115    84-214 (228)
  9 cd01226 PH_exo84 Exocyst compl  43.7      10 0.00026   19.4   0.9   21    8-28      5-25  (100)
 10 PRK13210 putative L-xylulose 5  41.7      31  0.0008   16.5   6.6  108    1-114    22-139 (284)
 11 TIGR02712 urea_carbox urea car  41.0      24 0.00062   17.1   2.6   73   12-86    383-462 (1226)
 12 KOG1708 consensus               37.5      13 0.00033   18.8   0.7   82   12-99     94-179 (236)
 13 pfam11325 DUF3127 Protein of u  30.2      34 0.00086   16.3   1.9   36   52-94     36-71  (84)
 14 TIGR01016 sucCoAbeta succinyl-  27.7      53  0.0014   15.1   2.6   25   80-107   341-365 (389)
 15 TIGR02362 dhaK1b probable dihy  26.8      56  0.0014   15.0   2.8   48   69-133    84-131 (328)
 16 TIGR01266 fum_ac_acetase fumar  26.6      33 0.00085   16.3   1.3   27   63-89    390-416 (436)
 17 KOG4270 consensus               26.5      56  0.0014   14.9   2.7   34  101-134   274-307 (577)
 18 PRK07508 para-aminobenzoate sy  25.7      58  0.0015   14.9   5.2   52   54-108   102-155 (377)
 19 TIGR00888 guaA_Nterm GMP synth  24.7      47  0.0012   15.4   1.8   26   86-112   168-193 (195)
 20 cd03068 PDI_b_ERp72 PDIb famil  24.1      62  0.0016   14.7   5.0   41   68-112     7-47  (107)
 21 KOG0238 consensus               23.9      63  0.0016   14.7   3.0   76   13-96    374-454 (670)
 22 pfam02679 ComA (2R)-phospho-3-  23.9      63  0.0016   14.7   7.5   97    1-111    91-197 (245)
 23 TIGR00827 EIIC-GAT PTS system,  22.0      37 0.00094   16.0   0.8   17   69-93    267-283 (407)
 24 pfam05763 DUF835 Protein of un  21.6      70  0.0018   14.4   5.2   67   59-134    54-121 (136)
 25 cd04375 RhoGAP_DLC1 RhoGAP_DLC  21.5      70  0.0018   14.4   2.5   39   96-134   123-161 (220)
 26 PRK03363 fixB putative electro  21.5      39 0.00099   15.9   0.8   23   89-112   201-223 (313)
 27 TIGR02062 RNase_B exoribonucle  21.1      53  0.0013   15.1   1.5   35   78-112    56-92  (664)
 28 COG3967 DltE Short-chain dehyd  20.8      23 0.00059   17.3  -0.4   19   67-85     17-35  (245)

No 1  
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=359.59  Aligned_cols=136  Identities=49%  Similarity=0.842  Sum_probs=133.9

Q ss_pred             CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCC
Q ss_conf             93378579949999887558779998457888888765432110022222002689740086799999999999960379
Q gi|254780320|r    1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGC   80 (136)
Q Consensus         1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~   80 (136)
                      |++|++.|||||+|||+|+||||||||||||+||++|+++|+|++|+.+++|||+|+|+||+|||++|++++++||++||
T Consensus        40 L~lA~e~~LDLV~Ispna~PPVcKImDYGKfkye~~KK~kEakKkQk~i~vKEik~rp~Id~hD~~~K~k~~~rFLe~Gd  119 (176)
T COG0290          40 LKLAEEAGLDLVEISPNAKPPVCKIMDYGKFKYEQKKKAKEAKKKQKQIQVKEIKLRPKIDEHDYETKLKNARRFLEKGD  119 (176)
T ss_pred             HHHHHHCCCCEEEECCCCCCCEEEEEECCCHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             99999759988998689999844862052067888888887762574577789996157573308999999999987698


Q ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCC
Q ss_conf             19999997097435735689999999998422432036773248769999920469
Q gi|254780320|r   81 KVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSKCV  136 (136)
Q Consensus        81 kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pkkv  136 (136)
                      +|||+|+|||||++|+|+|..+|++|.++++++|++|++|+++||+|+|+|+|++.
T Consensus       120 kVKvtirfrGRe~~h~elG~~vl~r~~~~~~~~~~ve~~pk~egr~m~m~laPkk~  175 (176)
T COG0290         120 KVKVTIRFRGREMAHQELGVKVLERVAEDLEDIAKVESEPKMEGRQMIMVLAPKKK  175 (176)
T ss_pred             EEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCCCCCEEEEEECCCCC
T ss_conf             59999998155560699999999999998654415512601178658999744668


No 2  
>CHL00199 infC translation initiation factor 3; Provisional
Probab=100.00  E-value=0  Score=357.46  Aligned_cols=136  Identities=44%  Similarity=0.684  Sum_probs=134.5

Q ss_pred             CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCC
Q ss_conf             93378579949999887558779998457888888765432110022222002689740086799999999999960379
Q gi|254780320|r    1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGC   80 (136)
Q Consensus         1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~   80 (136)
                      |++|+++|||||||||+|+||||||||||||+||++|++++++++|+.+++|||+|+|+|++|||++|+++|++||++||
T Consensus        46 l~~A~~~gLDLVevsp~a~PPVcKimDygK~~Ye~~Kk~k~~kkkq~~~~~KEir~~~~I~~hDl~~K~k~a~~FL~~G~  125 (182)
T CHL00199         46 LQLAKKQGLDLVLVSEKSDPPVCRIIDYGKYKFEQEKKAKEAKKKQHNSSIKEVKMRYKIEEHDYQVRINQAFKFLKAGD  125 (182)
T ss_pred             HHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             99999849988998899999878986556689999988776440467426666898756576389999999999986799


Q ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCC
Q ss_conf             19999997097435735689999999998422432036773248769999920469
Q gi|254780320|r   81 KVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSKCV  136 (136)
Q Consensus        81 kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pkkv  136 (136)
                      +|+|+|+|||||++|+|+|.++|++|+++|+++|.+|++|+++||+|+|+|+|+|+
T Consensus       126 kVKv~v~frGRE~~h~e~G~~ll~~~~~~l~~~~~ve~~pk~eGr~~~miL~PkK~  181 (182)
T CHL00199        126 KVKATLTFRGREIQHLSLAINLLNKMAADLSSIAEIQQPPSRDGRNMIMILSPKKV  181 (182)
T ss_pred             EEEEEEEEECHHHCCHHHHHHHHHHHHHHHHHHEEECCCCCCCCCEEEEEEECCCC
T ss_conf             69999998154432689999999999998541378604760008869999924757


No 3  
>PRK00028 infC translation initiation factor IF-3; Reviewed
Probab=100.00  E-value=0  Score=337.10  Aligned_cols=135  Identities=53%  Similarity=0.866  Sum_probs=133.3

Q ss_pred             CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCC
Q ss_conf             93378579949999887558779998457888888765432110022222002689740086799999999999960379
Q gi|254780320|r    1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGC   80 (136)
Q Consensus         1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~   80 (136)
                      |++|++.|||||+|||+++||||||||||||+|+++|+.++++++|+.+++|||+|+|+||+|||++|++++++||++||
T Consensus        39 l~~A~~~~LDLV~vs~~~~PPVcKi~dygK~~ye~~kk~k~~kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~  118 (175)
T PRK00028         39 LRLAEEAGLDLVEISPNAKPPVCKIMDYGKFKYEQQKKAKEAKKKQKVIEVKEIKLRPKIDEHDYQVKLKNARRFLEKGD  118 (175)
T ss_pred             HHHHHHCCCCEEEECCCCCCCEEEEEHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             99999819948998789999868985077899999988877652146532003578657560299999999999997799


Q ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECC
Q ss_conf             1999999709743573568999999999842243203677324876999992046
Q gi|254780320|r   81 KVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSKC  135 (136)
Q Consensus        81 kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pkk  135 (136)
                      +|+|+|+|||||++|+|+|.++|++|+++|+++|++|++|+++|++|+|+|+|+|
T Consensus       119 kVki~v~~rGRe~~~~e~g~~ll~~~~~~l~~i~~~e~~pk~~Gr~~~~~l~P~k  173 (175)
T PRK00028        119 KVKVTIRFRGREIAHKELGMELLERFAEDLEDIAKVEQEPKMEGRQMIMVLAPKK  173 (175)
T ss_pred             EEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHEEECCCCCCCCCEEEEEEECCC
T ss_conf             7999999877556588999999999999722245851477544875999991179


No 4  
>TIGR00168 infC translation initiation factor IF-3; InterPro: IPR001288   Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit . The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 . ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=99.97  E-value=3.4e-30  Score=201.06  Aligned_cols=135  Identities=45%  Similarity=0.788  Sum_probs=132.5

Q ss_pred             CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCC
Q ss_conf             93378579949999887558779998457888888765432110022222002689740086799999999999960379
Q gi|254780320|r    1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGC   80 (136)
Q Consensus         1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~   80 (136)
                      +.+|.+.+||||+++|++.||||+++|||+|.|++.++.++++++++...+||++++|.|+.||++++++++..|+++|+
T Consensus        29 ~~~~~~~~~dl~~~~~~~~pp~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~g~  108 (165)
T TIGR00168        29 LELAEEAGLDLVLVSPNAKPPVCKLLDYGKYKYEQEKKAKEAKKNQKVIELKEVKLRPTIDEHDLEFKLKNALGFLEKGD  108 (165)
T ss_pred             HHHHHHCCCCEEEECCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             76664316525763377887532211021023344555665543100111111001133221023456787777763587


Q ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCEEEEEEEECC
Q ss_conf             1999999709743573568999999999842243203677-324876999992046
Q gi|254780320|r   81 KVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEP-KFEGRQMIMILSSKC  135 (136)
Q Consensus        81 kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~p-k~~Gr~~~~~l~Pkk  135 (136)
                      +++++++|+||+.+|.+.|..+++++...+.+++.++..| +.+|+.+.+++.|++
T Consensus       109 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~p~~  164 (165)
T TIGR00168       109 KVKFTVRFRGRELTHSELGLDVLDRFLEDLADLAEVEKPPTKLEGRSLFLLLAPKK  164 (165)
T ss_pred             EEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCC
T ss_conf             04788763230345778889999999987666654322110110102334430346


No 5  
>pfam00707 IF3_C Translation initiation factor IF-3, C-terminal domain.
Probab=99.96  E-value=5e-30  Score=200.05  Aligned_cols=87  Identities=52%  Similarity=0.866  Sum_probs=85.1

Q ss_pred             CCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE
Q ss_conf             22200268974008679999999999996037919999997097435735689999999998422432036773248769
Q gi|254780320|r   48 STGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQM  127 (136)
Q Consensus        48 ~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~  127 (136)
                      .+++|||||+|+||+|||++|+++|++||++||+||++|+|||||++|+|.|.++|++|+++++++|.+|++|+++||+|
T Consensus         1 ~v~~KEir~~~~I~~hDl~~K~k~a~~FL~~G~kVKv~i~frGRE~~~~e~g~~~l~~i~~~l~~~~~ve~~pk~eGr~~   80 (87)
T pfam00707         1 VVQVKEIKLRPKIDEHDLEVKLKHARKFLEKGDKVKVTIRFRGREIAHPELGRELLDRFAEDLEDIATVEKPPKMEGRNM   80 (87)
T ss_pred             CEEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHEEECCCCCCCCCEE
T ss_conf             95778999726877015999999999999779949999998487565889999999999998551537515876548759


Q ss_pred             EEEEEEC
Q ss_conf             9999204
Q gi|254780320|r  128 IMILSSK  134 (136)
Q Consensus       128 ~~~l~Pk  134 (136)
                      +|+|+|+
T Consensus        81 ~~~l~Pk   87 (87)
T pfam00707        81 TMILAPK   87 (87)
T ss_pred             EEEEECC
T ss_conf             9999369


No 6  
>pfam05198 IF3_N Translation initiation factor IF-3, N-terminal domain.
Probab=99.69  E-value=1.9e-17  Score=125.01  Aligned_cols=43  Identities=49%  Similarity=0.828  Sum_probs=40.7

Q ss_pred             CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHH
Q ss_conf             9337857994999988755877999845788888876543211
Q gi|254780320|r    1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEAR   43 (136)
Q Consensus         1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~K   43 (136)
                      |++|++.|||||+|||+++||||||||||||+|+++|+.+++|
T Consensus        34 l~~A~~~~LDLV~vs~~a~PPVcki~DygK~~ye~~kk~ke~k   76 (76)
T pfam05198        34 LRLAEEKGLDLVEISPNADPPVCKIMDYGKFKYEQQKKAKEAK   76 (76)
T ss_pred             HHHHHHCCCCEEEECCCCCCCEEEEEECCHHHHHHHHHHHHCC
T ss_conf             9999984996899899999988899627118999998786519


No 7  
>pfam06152 Phage_min_cap2 Phage minor capsid protein 2. Family of related phage minor capsid proteins.
Probab=56.21  E-value=7.1  Score=20.32  Aligned_cols=25  Identities=24%  Similarity=0.418  Sum_probs=18.1

Q ss_pred             HHHHHCCCCEEEECCCCCC-CEEEEE
Q ss_conf             3378579949999887558-779998
Q gi|254780320|r    2 QMAQEANLDLVEIDSSVTP-SVCKIL   26 (136)
Q Consensus         2 ~~A~~~~lDLV~vs~~~~P-PVcKi~   26 (136)
                      +.+++.|.|||+||..+.+ |-|-..
T Consensus       217 ~~~~e~g~d~v~vS~H~garp~capw  242 (361)
T pfam06152       217 KRMEEYGVDLVVVSSHAGARPACAPI  242 (361)
T ss_pred             HHHHHCCCCEEEECCCCCCCCCCCCC
T ss_conf             67998198089970787889887770


No 8  
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=45.36  E-value=10  Score=19.39  Aligned_cols=96  Identities=17%  Similarity=0.272  Sum_probs=50.9

Q ss_pred             CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHH-----------------------HHHHHHCCCCCCCEEEEEE
Q ss_conf             93378579949999887558779998457888888765-----------------------4321100222220026897
Q gi|254780320|r    1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKN-----------------------AVEARKKQKSTGIKEVKMR   57 (136)
Q Consensus         1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk-----------------------~k~~Kkkq~~~~~KEir~~   57 (136)
                      +++|++.|.|+|-|| +++|-+|+     .+.-|.---                       +-.++-+      --+|.+
T Consensus        84 ~ei~K~~g~d~vRiS-G~EP~l~~-----EHvlevIeLl~~~tFvlETNG~~~g~drslv~el~nr~n------v~vRVs  151 (228)
T COG5014          84 LEISKKRGCDLVRIS-GAEPILGR-----EHVLEVIELLVNNTFVLETNGLMFGFDRSLVDELVNRLN------VLVRVS  151 (228)
T ss_pred             HHHHHHCCCCEEEEE-CCCCCCCH-----HHHHHHHHHCCCCEEEEEECCEEEECCHHHHHHHHCCCC------EEEEEE
T ss_conf             999885588689962-89864468-----999999986347649997577688358889999713786------399998


Q ss_pred             EE------------CCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             40------------08679999999999996037919999997097435735689999999998422432
Q gi|254780320|r   58 PV------------IDLHDLQVKLKAIDGFLRDGCKVKISVKFRGREIMHQDLGRELLSNIKERFGEISR  115 (136)
Q Consensus        58 ~~------------I~~hDl~~K~k~~~~FL~~G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~  115 (136)
                      .+            ....-+...++..+-..++|+++-..+.. +   ..+|-+.   .++...|+|.+.
T Consensus       152 vKG~dpesF~kIT~asp~~F~~QL~aLr~L~~~g~rf~pA~~~-~---f~~Ed~~---k~Lak~Lgehp~  214 (228)
T COG5014         152 VKGWDPESFEKITGASPEYFRYQLKALRHLHGKGHRFWPAVVY-D---FFREDGL---KELAKRLGEHPP  214 (228)
T ss_pred             ECCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEEHHHH-C---CCHHHHH---HHHHHHHCCCCC
T ss_conf             3579889989875689278999999999998467165101432-0---3513668---999987543899


No 9  
>cd01226 PH_exo84 Exocyst complex 84-kDa subunit Pleckstrin Homology (PH) domain. Exo84 is a subunit of the exocyt complex, which is important in intracellular trafficking.  In metazoa, Exo84 has a PH domain towards its N-terminus. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding.  Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=43.67  E-value=10  Score=19.41  Aligned_cols=21  Identities=19%  Similarity=0.240  Sum_probs=17.9

Q ss_pred             CCCEEEECCCCCCCEEEEEEH
Q ss_conf             994999988755877999845
Q gi|254780320|r    8 NLDLVEIDSSVTPSVCKILDL   28 (136)
Q Consensus         8 ~lDLV~vs~~~~PPVcKi~dy   28 (136)
                      +=||+|++|+..-||||++-|
T Consensus         5 ~G~L~ElD~~~~~~i~~v~~f   25 (100)
T cd01226           5 YGELEEFDVETKKPVQRVMLF   25 (100)
T ss_pred             CCCEEEECCCCCCHHHHEEEE
T ss_conf             483699767667666621115


No 10 
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=41.73  E-value=31  Score=16.46  Aligned_cols=108  Identities=15%  Similarity=0.220  Sum_probs=51.8

Q ss_pred             CHHHHHCCCCEEEECCCC-CCCEEEEEEHHHH-HHHHHHHHHHHHHCCCCCCCEEEEEEEE----CCHHHHHHHH---HH
Q ss_conf             933785799499998875-5877999845788-8888765432110022222002689740----0867999999---99
Q gi|254780320|r    1 MQMAQEANLDLVEIDSSV-TPSVCKILDLRKL-RYTIQKNAVEARKKQKSTGIKEVKMRPV----IDLHDLQVKL---KA   71 (136)
Q Consensus         1 l~~A~~~~lDLV~vs~~~-~PPVcKi~dygK~-~ye~~Kk~k~~Kkkq~~~~~KEir~~~~----I~~hDl~~K~---k~   71 (136)
                      +++|++.|+|.||+|-+- +..+.++ |+++. +.+..+..     ....+.+-.+-++..    .+..|-.++-   ..
T Consensus        22 f~~Ak~~Gfd~IE~siDe~d~~~~~l-~~~~~~~~~i~~~~-----~~~gl~I~s~~~s~~~~~pl~s~d~~~r~~~le~   95 (284)
T PRK13210         22 LVLAKECGFDFVEMSVDETDERLARL-DWSKEERLELVKAI-----YETGVRIPSMCLSAHRRFPFGSRDEATRERALEI   95 (284)
T ss_pred             HHHHHHCCCCEEEEECCCCCCCCCCC-CCCHHHHHHHHHHH-----HHCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             99999869988999606754222578-99989999999999-----9829835664155666899999898999999999


Q ss_pred             HHHHHCCCCCEEEEE-EECCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             999960379199999-9709743573568999999999842243
Q gi|254780320|r   72 IDGFLRDGCKVKISV-KFRGREIMHQDLGRELLSNIKERFGEIS  114 (136)
Q Consensus        72 ~~~FL~~G~kVki~i-~frGRe~~~~e~g~~~l~~i~~~l~~~~  114 (136)
                      +++.++-..+.-+.+ .+-|-...+.+.-.+..+++++.+..++
T Consensus        96 l~kaI~lA~~LGi~~I~l~g~dv~~~~~~~~~~~rf~e~l~~~~  139 (284)
T PRK13210         96 MKKAIRLAQDLGIRTIQLAGYDVYYEEKDEETRQRFIEGLAWAV  139 (284)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             99999999980997899688766668698899999999999999


No 11 
>TIGR02712 urea_carbox urea carboxylase; InterPro: IPR014084   Members of this family are ATP-dependent urea carboxylases, including characterised members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae (Baker's yeast). The allophanate hydrolase domain of the yeast enzyme is not included in this entry and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from O. sagaranensis was shown to be highly active on acetamide and formamide as well as urea..
Probab=41.01  E-value=24  Score=17.13  Aligned_cols=73  Identities=15%  Similarity=0.229  Sum_probs=44.4

Q ss_pred             EEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCC----CC---CEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             9998875587799984578888887654321100222----22---0026897400867999999999999603791999
Q gi|254780320|r   12 VEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKS----TG---IKEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKI   84 (136)
Q Consensus        12 V~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~----~~---~KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki   84 (136)
                      .+|||.=+|-++||+-||+-|-+.-.+..+|=...+.    |.   +|.|-.+..-......|++  +..|--..+.|+|
T Consensus       383 tevsp~YDPmlAKiIv~g~~R~~A~~kL~~AL~~T~v~Gi~TNLdYLr~i~~s~~F~~g~~sT~~--L~~~~y~~~~iEv  460 (1226)
T TIGR02712       383 TEVSPEYDPMLAKIIVHGKDREDAIAKLSQALDETRVYGIETNLDYLRSILSSEVFRSGQVSTRL--LNSFVYTPPAIEV  460 (1226)
T ss_pred             CEECCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCEEEEECHHHHHHHHCCHHHHHHHHHHHH--HCCCCCCCCEEEE
T ss_conf             35677658742446643679789999999887301012354247899988401334102577664--0053546765788


Q ss_pred             EE
Q ss_conf             99
Q gi|254780320|r   85 SV   86 (136)
Q Consensus        85 ~i   86 (136)
                      ..
T Consensus       461 ~~  462 (1226)
T TIGR02712       461 LE  462 (1226)
T ss_pred             EC
T ss_conf             64


No 12 
>KOG1708 consensus
Probab=37.51  E-value=13  Score=18.79  Aligned_cols=82  Identities=24%  Similarity=0.151  Sum_probs=45.4

Q ss_pred             EEECCCCCCCEEEEEEHHHHHHHHHHHHHHHH----HCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             99988755877999845788888876543211----00222220026897400867999999999999603791999999
Q gi|254780320|r   12 VEIDSSVTPSVCKILDLRKLRYTIQKNAVEAR----KKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISVK   87 (136)
Q Consensus        12 V~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~K----kkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i~   87 (136)
                      +.|.++.+--|.+=++ -||+|.-..++-+-.    .-+.-..-|++.+-   |.+|.+. ..---+|+++|-+|+++++
T Consensus        94 tqv~r~~s~VvV~gln-~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLv---dp~d~q~-te~~wr~~e~GekVRvstr  168 (236)
T KOG1708          94 TQVIRHRSWVVVKGLN-TKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLV---DPEDDQP-TEVEWRFTEDGEKVRVSTR  168 (236)
T ss_pred             EEEEECCCEEEECCCC-HHHHHHCCCCCCCCCEEEEECCCCEEECCEEEE---CCCCCCC-CEEEEEECCCCCEEEEEEC
T ss_conf             9986047648972610-344442640028886277503772340406987---7323677-3201577478857999830


Q ss_pred             ECCCCCCCHHHH
Q ss_conf             709743573568
Q gi|254780320|r   88 FRGREIMHQDLG   99 (136)
Q Consensus        88 frGRe~~~~e~g   99 (136)
                       -||.+..+|..
T Consensus       169 -SG~iIpipe~~  179 (236)
T KOG1708         169 -SGRIIPIPEKW  179 (236)
T ss_pred             -CCCCCCCCCCC
T ss_conf             -55161475535


No 13 
>pfam11325 DUF3127 Protein of unknown function (DUF3127). This bacterial family of proteins has no known function.
Probab=30.22  E-value=34  Score=16.26  Aligned_cols=36  Identities=31%  Similarity=0.285  Sum_probs=24.4

Q ss_pred             EEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCC
Q ss_conf             0268974008679999999999996037919999997097435
Q gi|254780320|r   52 KEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISVKFRGREIM   94 (136)
Q Consensus        52 KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i~frGRe~~   94 (136)
                      ..|.|...=|.-|+-..       +.-|+.|+|+...+|||-.
T Consensus        36 ~~i~fe~~~dk~~~~~~-------~~vGd~V~V~fnl~gREw~   71 (84)
T pfam11325        36 QKICFEFWGDKIDLLDS-------LNVGDEVKVSFDLEGREWN   71 (84)
T ss_pred             CEEEEEEECCCHHHHCC-------CCCCCEEEEEEEEECCEEC
T ss_conf             73899998367567706-------8999989999982536815


No 14 
>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit; InterPro: IPR005809   There are four different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are: ATP citrate-lyase (4.1.3.8 from EC) , the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. ATP-citrate lyase is a tetramer of identical subunits; Succinyl-CoA ligase (GDP-forming) (6.2.1.4 from EC)  is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits; Succinyl-CoA ligase (ADP-forming) (6.2.1.5 from EC)  is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits; and Malate-CoA ligase (6.2.1.9 from EC) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits.   This entry corresponds to a conserved region located in the first half of ATP citrate lyase and in the beta subunits of succinyl-CoA ligases and malate-CoA ligase. ; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=27.72  E-value=53  Score=15.08  Aligned_cols=25  Identities=20%  Similarity=0.472  Sum_probs=16.0

Q ss_pred             CCEEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             9199999970974357356899999999
Q gi|254780320|r   80 CKVKISVKFRGREIMHQDLGRELLSNIK  107 (136)
Q Consensus        80 ~kVki~i~frGRe~~~~e~g~~~l~~i~  107 (136)
                      -+|.++||+-|   ++.|.|+++|...-
T Consensus       341 ~~VP~VvRL~G---TN~E~G~~iL~e~g  365 (389)
T TIGR01016       341 VNVPVVVRLEG---TNVEEGKKILQESG  365 (389)
T ss_pred             CCCCEEEECCC---CCHHHHHHHHHHHC
T ss_conf             53687898157---88788889999727


No 15 
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit; InterPro: IPR012735    Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated 2.7.1.29 from EC. By contract, Escherichia coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex..
Probab=26.79  E-value=56  Score=14.98  Aligned_cols=48  Identities=21%  Similarity=0.256  Sum_probs=34.7

Q ss_pred             HHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEE
Q ss_conf             99999996037919999997097435735689999999998422432036773248769999920
Q gi|254780320|r   69 LKAIDGFLRDGCKVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSS  133 (136)
Q Consensus        69 ~k~~~~FL~~G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~P  133 (136)
                      +=.+.+|+++|..|=+.|+                 .|..||++...-+...+.||++.--+++-
T Consensus        84 il~~~r~~~~gkGVf~IiK-----------------NF~AD~~~F~~A~~qar~EG~~~~~~iv~  131 (328)
T TIGR02362        84 ILEAIRQVDRGKGVFVIIK-----------------NFEADLSEFSQAIEQARQEGRDIKYIIVH  131 (328)
T ss_pred             HHHHHHHHHCCCEEEEEEE-----------------CCHHHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             9999987524976899971-----------------76777899999999998638950379972


No 16 
>TIGR01266 fum_ac_acetase fumarylacetoacetase; InterPro: IPR005959   Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation . This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders , . The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole . FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures .; GO: 0004334 fumarylacetoacetase activity, 0009072 aromatic amino acid family metabolic process.
Probab=26.61  E-value=33  Score=16.32  Aligned_cols=27  Identities=19%  Similarity=0.236  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             799999999999960379199999970
Q gi|254780320|r   63 HDLQVKLKAIDGFLRDGCKVKISVKFR   89 (136)
Q Consensus        63 hDl~~K~k~~~~FL~~G~kVki~i~fr   89 (136)
                      +..++=--+.|+||+|||-|-++=+..
T Consensus       390 ~~v~la~g~~R~FL~DGDeVil~g~c~  416 (436)
T TIGR01266       390 KPVKLADGETRKFLEDGDEVILRGVCK  416 (436)
T ss_pred             CCEECCCCCCCCCCCCCCEEEEEEEEC
T ss_conf             411137875132002688699987864


No 17 
>KOG4270 consensus
Probab=26.50  E-value=56  Score=14.95  Aligned_cols=34  Identities=12%  Similarity=0.303  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEC
Q ss_conf             9999999984224320367732487699999204
Q gi|254780320|r  101 ELLSNIKERFGEISRIDCEPKFEGRQMIMILSSK  134 (136)
Q Consensus       101 ~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pk  134 (136)
                      .+|+-++..+++++.-+.-+||.-+++-|+++|+
T Consensus       274 slL~yli~flA~v~~~~~vNKMs~~NlAiV~gPN  307 (577)
T KOG4270         274 SLLRYLIRFLADVVEKEHVNKMSARNLAIVFGPN  307 (577)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHCEEEECCC
T ss_conf             8899999999998887650246611100574577


No 18 
>PRK07508 para-aminobenzoate synthase component I; Provisional
Probab=25.74  E-value=58  Score=14.87  Aligned_cols=52  Identities=12%  Similarity=0.107  Sum_probs=37.2

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEE--EECCCCCCCHHHHHHHHHHHHH
Q ss_conf             689740086799999999999960379199999--9709743573568999999999
Q gi|254780320|r   54 VKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISV--KFRGREIMHQDLGRELLSNIKE  108 (136)
Q Consensus        54 ir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i--~frGRe~~~~e~g~~~l~~i~~  108 (136)
                      ..+.+.++.-||.-++.++++++..|+--.+.+  +|+++-...+   ..++.++..
T Consensus       102 ~~~~~~~~~~~Y~~~v~~ik~~I~~Gd~YQvnlt~~~~~~~~~~p---~~ly~~Lr~  155 (377)
T PRK07508        102 RDPVARWDFADYAARFERLHRHIRAGDCYQANLTFPVDARWEGDP---LALYRALAA  155 (377)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEECCCCH---HHHHHHHHH
T ss_conf             688778999999999999999997598899980599998168999---999999822


No 19 
>TIGR00888 guaA_Nterm GMP synthase, N-terminal domain; InterPro: IPR004739   The N-terminal region of GMP synthase 6.3.5.2 from EC is recognised by this signature. GMP synthase catalyzes the synthesis of GMP from XMP , .  ATP + xanthosine 5'-phosphate + L-glutamine + H(2)O = AMP + diphosphate + GMP + L-glutamate ; GO: 0003922 GMP synthase (glutamine-hydrolyzing) activity, 0005524 ATP binding, 0006177 GMP biosynthetic process.
Probab=24.68  E-value=47  Score=15.43  Aligned_cols=26  Identities=35%  Similarity=0.616  Sum_probs=20.0

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             997097435735689999999998422
Q gi|254780320|r   86 VKFRGREIMHQDLGRELLSNIKERFGE  112 (136)
Q Consensus        86 i~frGRe~~~~e~g~~~l~~i~~~l~~  112 (136)
                      |.|.- |.+|.+.|.++|.+|+.++..
T Consensus       168 VQFHP-EV~Ht~~G~~~L~NF~~~~C~  193 (195)
T TIGR00888       168 VQFHP-EVTHTEYGKELLKNFVKDVCG  193 (195)
T ss_pred             EEECC-CEEECHHHHHHHHHHHHHHCC
T ss_conf             65178-312153457899988876315


No 20 
>cd03068 PDI_b_ERp72 PDIb family, ERp72 subfamily, first redox inactive TRX-like domain b; ERp72 exhibits both disulfide oxidase and reductase functions like PDI, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER and acting as isomerases to correct any non-native disulfide bonds. It also displays chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. ERp72 contains three redox-active TRX (a) domains and two redox inactive TRX-like (b) domains.  Its molecular structure is a"abb'a', compared to the abb'a' structure of PDI. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. Similar to PDI, the b domain of ERp72 is likely involved in binding to substrates.
Probab=24.14  E-value=62  Score=14.68  Aligned_cols=41  Identities=34%  Similarity=0.450  Sum_probs=30.4

Q ss_pred             HHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             999999996037919999997097435735689999999998422
Q gi|254780320|r   68 KLKAIDGFLRDGCKVKISVKFRGREIMHQDLGRELLSNIKERFGE  112 (136)
Q Consensus        68 K~k~~~~FL~~G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~  112 (136)
                      -++++++||.+|+-|.|+=.|.|-.-.    ..+.+.+.++.+.+
T Consensus         7 s~~~~~~fl~d~ddv~VVGfF~~~ds~----~~~~FlkaA~~lRe   47 (107)
T cd03068           7 TLKQVQEFLRDGDDVIIIGVFSGEEDP----AYQLYQDAANSLRE   47 (107)
T ss_pred             HHHHHHHHHCCCCCEEEEEEECCCCCH----HHHHHHHHHHHCCC
T ss_conf             099999985378870899998689977----89999999985505


No 21 
>KOG0238 consensus
Probab=23.93  E-value=63  Score=14.66  Aligned_cols=76  Identities=17%  Similarity=0.151  Sum_probs=44.7

Q ss_pred             EECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEE-----E
Q ss_conf             99887558779998457888888765432110022222002689740086799999999999960379199999-----9
Q gi|254780320|r   13 EIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISV-----K   87 (136)
Q Consensus        13 ~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i-----~   87 (136)
                      +||+.-+|.+|||+.||+-+-+.-.+.+.+-        -+-.++--+..=||-..+-...+|-...-..++.-     .
T Consensus       374 ~vs~~YDpmiaKlvvwg~dR~~Al~kl~~aL--------~~~~I~Gv~tnI~~l~~i~~~~~F~~g~V~T~fi~~~~~el  445 (670)
T KOG0238         374 EVSIHYDPMIAKLVVWGKDREEALNKLKDAL--------DNYVIRGVPTNIDFLRDIISHPEFAKGNVSTKFIPEHQPEL  445 (670)
T ss_pred             CCCCCCCCHHEEEEEECCCHHHHHHHHHHHH--------HHCEEECCCCCHHHHHHHHCCHHHHCCCCCCCCCHHCCCCC
T ss_conf             4461136500156676487899999999998--------60688467566689998754766632763015340107444


Q ss_pred             ECCCCCCCH
Q ss_conf             709743573
Q gi|254780320|r   88 FRGREIMHQ   96 (136)
Q Consensus        88 frGRe~~~~   96 (136)
                      |.++...-.
T Consensus       446 f~~~~~~~~  454 (670)
T KOG0238         446 FAPESITPA  454 (670)
T ss_pred             CCCCCCCCH
T ss_conf             675235827


No 22 
>pfam02679 ComA (2R)-phospho-3-sulfolactate synthase (ComA). In methanobacteria (2R)-phospho-3-sulfolactate synthase (ComA) catalyses the first step of the biosynthesis of coenzyme M from phosphoenolpyruvate (P-enolpyruvate). This novel enzyme catalyses the stereospecific Michael addition of sulfite to P-enolpyruvate, forming L-2-phospho-3-sulfolactate (PSL). It is suggested that the ComA-catalysed reaction is analogous to those reactions catalysed by beta-elimination enzymes that proceed through an enolate intermediate.
Probab=23.90  E-value=63  Score=14.66  Aligned_cols=97  Identities=20%  Similarity=0.282  Sum_probs=50.9

Q ss_pred             CHHHHHCCCCEEEECCCCCC-CEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEE--EECCHHHHHHHHHHHHHHHC
Q ss_conf             93378579949999887558-7799984578888887654321100222220026897--40086799999999999960
Q gi|254780320|r    1 MQMAQEANLDLVEIDSSVTP-SVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMR--PVIDLHDLQVKLKAIDGFLR   77 (136)
Q Consensus         1 l~~A~~~~lDLV~vs~~~~P-PVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~--~~I~~hDl~~K~k~~~~FL~   77 (136)
                      ++.+++.|+|-||||.++-. |       ...+-+.-++.++.    --..+=|+--.  -.....+.+-.+++++.||+
T Consensus        91 ~~~~~~lGf~~iEiSdg~i~i~-------~~~~~~~I~~~~~~----G~~v~~EvG~K~~~~~~~~~~~~~I~~~~~~Le  159 (245)
T pfam02679        91 LRECKELGFDAIEISDGSIELP-------EEERLRLIRKAKKA----GFKVLSEVGKKDPEADSELTPDELIEQIERDLE  159 (245)
T ss_pred             HHHHHHCCCCEEEECCCCCCCC-------HHHHHHHHHHHHHC----CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             9999986998899568844689-------89999999999978----997966415467543456799999999999997


Q ss_pred             CCCCEEEEEEECCCC----CCCH---HHHHHHHHHHHHHHH
Q ss_conf             379199999970974----3573---568999999999842
Q gi|254780320|r   78 DGCKVKISVKFRGRE----IMHQ---DLGRELLSNIKERFG  111 (136)
Q Consensus        78 ~G~kVki~i~frGRe----~~~~---e~g~~~l~~i~~~l~  111 (136)
                      .|--- |.+  -+||    -.+.   +.-..++++|++.+.
T Consensus       160 aGA~~-Vii--EarEsg~~Gi~~~~g~~r~~~i~~I~~~~~  197 (245)
T pfam02679       160 AGADK-VII--EARESGGVGLYDSDGEVRTDLVEEILERLG  197 (245)
T ss_pred             CCCCE-EEE--ECCCCCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             69828-998--510148756508898871889999997388


No 23 
>TIGR00827 EIIC-GAT PTS system, galactitol-specific IIC component; InterPro: IPR013853 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.    The only characterised member of this family of PTS transporters is the Escherichia coli galactitol transporter. Gat family PTS systems typically have 3 components: IIA, IIB and IIC.    This family is specific for the IIC component of the PTS Gat family. It contains fewer proteins than IPR004703 from INTERPRO..
Probab=22.02  E-value=37  Score=16.03  Aligned_cols=17  Identities=41%  Similarity=0.755  Sum_probs=10.7

Q ss_pred             HHHHHHHHCCCCCEEEEEEECCCCC
Q ss_conf             9999999603791999999709743
Q gi|254780320|r   69 LKAIDGFLRDGCKVKISVKFRGREI   93 (136)
Q Consensus        69 ~k~~~~FL~~G~kVki~i~frGRe~   93 (136)
                      .++||+||++        +|+|||.
T Consensus       267 s~~AR~~lqk--------~FggrE~  283 (407)
T TIGR00827       267 SESAREFLQK--------KFGGREV  283 (407)
T ss_pred             HHHHHHHHHH--------HHCCEEE
T ss_conf             2788999975--------5288058


No 24 
>pfam05763 DUF835 Protein of unknown function (DUF835). The members of this archaebacterial protein family are around 250-300 amino acid residues in length. The function of these proteins is not known.
Probab=21.59  E-value=70  Score=14.38  Aligned_cols=67  Identities=19%  Similarity=0.310  Sum_probs=52.1

Q ss_pred             ECCHHHHHHHHHHHHHHHCC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEC
Q ss_conf             00867999999999999603-79199999970974357356899999999984224320367732487699999204
Q gi|254780320|r   59 VIDLHDLQVKLKAIDGFLRD-GCKVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSK  134 (136)
Q Consensus        59 ~I~~hDl~~K~k~~~~FL~~-G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pk  134 (136)
                      .|+..+|..-...+.+||+. |+.   +|.+-|=|.---+.|.+-+-+|+..+.|.+..      .|..++..+.|.
T Consensus        54 ~i~Pt~L~~l~~~i~~fl~~~~~~---vV~iDglEYLil~NgF~~v~KfL~~lkD~~~~------~~~~lil~~d~~  121 (136)
T pfam05763        54 AISPTNLHKLLDLIARFLKKNGNG---VVLIDGLEYLVLENGFESVAKFLLSLKDYAIL------HNGTLILVVDPE  121 (136)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCC---EEEEECHHHHHHHCCHHHHHHHHHHHHHHHHH------CCCEEEEEECHH
T ss_conf             659754599999999999968995---89991478999971879999999997899835------499899997833


No 25 
>cd04375 RhoGAP_DLC1 RhoGAP_DLC1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of DLC1-like proteins. DLC1 shows in vitro GAP activity towards RhoA and CDC42. Beside its C-terminal GAP domain, DLC1 also contains a SAM (sterile alpha motif) and a START (StAR-related lipid transfer action) domain. DLC1 has tumor suppressor activity in cell culture. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=21.52  E-value=70  Score=14.37  Aligned_cols=39  Identities=15%  Similarity=0.262  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEC
Q ss_conf             356899999999984224320367732487699999204
Q gi|254780320|r   96 QDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSK  134 (136)
Q Consensus        96 ~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pk  134 (136)
                      |+.-+++|..+...|..++.-...-+|.-.++.++++|+
T Consensus       123 P~~n~~~L~~Ll~fL~~V~~~s~~NkMt~~NLAivfaPn  161 (220)
T cd04375         123 PDENREVLQTLLYFLSDVAANSQENQMTATNLAVCLAPS  161 (220)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHEEECHH
T ss_conf             999999999999999999971764579747711000105


No 26 
>PRK03363 fixB putative electron transfer flavoprotein FixB; Provisional
Probab=21.48  E-value=39  Score=15.92  Aligned_cols=23  Identities=22%  Similarity=0.284  Sum_probs=14.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             097435735689999999998422
Q gi|254780320|r   89 RGREIMHQDLGRELLSNIKERFGE  112 (136)
Q Consensus        89 rGRe~~~~e~g~~~l~~i~~~l~~  112 (136)
                      =||-+..+|. ..++..+.+.|..
T Consensus       201 gGRG~~~~e~-~~l~~eLA~~LGa  223 (313)
T PRK03363        201 VGRGIGSKEN-IALAEQLCKAIGA  223 (313)
T ss_pred             CCCCCCCCHH-HHHHHHHHHHHCC
T ss_conf             4876578234-7999999998486


No 27 
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804    This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=21.08  E-value=53  Score=15.11  Aligned_cols=35  Identities=17%  Similarity=0.229  Sum_probs=26.9

Q ss_pred             CCCCEEEEEEE-CCCCCCCHHHH-HHHHHHHHHHHHH
Q ss_conf             37919999997-09743573568-9999999998422
Q gi|254780320|r   78 DGCKVKISVKF-RGREIMHQDLG-RELLSNIKERFGE  112 (136)
Q Consensus        78 ~G~kVki~i~f-rGRe~~~~e~g-~~~l~~i~~~l~~  112 (136)
                      .||||..+|.- +-||.+-||.- ...|.||+.-+..
T Consensus        56 HGDki~A~i~~e~drE~AEPe~LiEp~LtRFvgkv~~   92 (664)
T TIGR02062        56 HGDKIVAVIKKEKDREVAEPEELIEPFLTRFVGKVKL   92 (664)
T ss_pred             CCCEEEEEEEECCCCCCCCCHHHHHHHHCCEEEEEEE
T ss_conf             4882799997358712148434310211234777873


No 28 
>COG3967 DltE Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane]
Probab=20.78  E-value=23  Score=17.26  Aligned_cols=19  Identities=32%  Similarity=0.366  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHCCCCCEEEE
Q ss_conf             9999999996037919999
Q gi|254780320|r   67 VKLKAIDGFLRDGCKVKIS   85 (136)
Q Consensus        67 ~K~k~~~~FL~~G~kVki~   85 (136)
                      +-+.-+++|++-||+|-|.
T Consensus        17 IGl~lak~f~elgN~VIi~   35 (245)
T COG3967          17 IGLALAKRFLELGNTVIIC   35 (245)
T ss_pred             HHHHHHHHHHHHCCEEEEE
T ss_conf             6599999999838979996


Done!